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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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jfy133 and mashehu authored Jan 27, 2023
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4 changes: 2 additions & 2 deletions nf_core/pipeline-template/docs/usage.md
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Expand Up @@ -79,7 +79,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than

Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.

> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) and other infrastructural tweaks.
> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) and other infrastructural tweaks.
> The above pipeline run specified with a params file in yaml format:
```bash
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This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.

To further assist in reproducbility, you can use share and re-use [params files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.

> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
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